matplotlib-users Mailing List for matplotlib

I'm trying to find a matplotlib 0.99.3 binary installer that works with 
the standard python.org Python (preferably 2.6) and hence works with Mac 
OS X 10.4 or greater. (I distribute an application that needs to run on 
a wide range of versions of Mac OS X).

The official binary I found refuses to install on my machine claiming it 
wants system python 2.6 (I happen to be running 10.5 so that's no use to 
me, and some users of my application are running 10.4).

I also tried the egg, but of course it fails -- presumably it's based on 
the same build.

If a binary isn't available I"ll make my own, but I figured I'd check 
first.

-- Russell

I have a non-matplotlib related project that requires usage of GSHHS dataset shapefiles.
The regular GSHHS dataset doesnt appear to include political boundaries, however the GSHHS dataset used by matplotlib/basemap does include country/border data. I'd like to extract  matplotlib/basemap GSHHS country data & convert it to shapefile format.

specifically, the following files that are included with matplotlib/basemap:
countries_c.dat
countries_f.dat
countries_h.dat
countries_i.dat
countries_l.dat
countriesmeta_c.dat 
countriesmeta_f.dat
countriesmeta_h.dat
countriesmeta_i.dat
countriesmeta_l.dat

how can I convert these files to shapefile format, or where can I get shapefiles that already include this data & that are based on the GSHHS coastline data?

please help,
thanks,
P.Romero


 		 	   		  
_________________________________________________________________
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On 06/30/2010 10:40 AM, magnus_p wrote:
>
> I am trying to plot a spectrum, with lower x axis = velocity, on the upper =
> frequency
>
> The relationship between them (doppler formula) is
> f = (1-v/c)*f_0
> where f is the resulting frequency, v the velocity, c the speed of light,
> and f_0 the frequency at v=0, ie. the v_lsr.
>
> I have tried to solve it by looking at
> http://matplotlib.sourceforge.net/examples/axes_grid/parasite_simple2.html
> http://matplotlib.sourceforge.net/examples/axes_grid/parasite_simple2.html
> , where it is solved by
>
> pm_to_kms = 1./206265.*2300*3.085e18/3.15e7/1.e5
> aux_trans = matplotlib.transforms.Affine2D().scale(pm_to_kms, 1.)
> ax_pm = ax_kms.twin(aux_trans)
> ax_pm.set_viewlim_mode("transform")
>
> well, my problem is that it is not a simple scaling law, but a linear
> function.
>
> Anyone know how to solve this?
>
> Magnus

I had a similar problem when I needed to plot some data in terms of 
frequency and wavelength. See the attached example script.

Regards,
João Silva

Hello,

I have a subplot with 4 lines.
I display the legend.
I can remove a line easily with something like del(self.ax.lines[n]).
But how can I remove the line in the legend ?

I found that I can remove all the lines, add news ones, but all the
lines (new and deleted) remain in the legend.

thanks for helping

Philippe

I am trying to plot some data over  a mesh using the plot_surface
method.  However when I plot my data, everything is the same color
when I expected to get a nice rainbow of colors as in the example:
http://matplotlib.sourceforge.net/examples/mplot3d/surface3d_demo.html

I have attached a simple script to show what I did as well as the
result.  Essentially, I just copied the above demo, but put my own
data in.  I think the problem arises because I have "holes" in my
data, or areas where the data is zero.  These zeros throw the scaling
off so I tried to eliminate their effect, but this messed everything
up.

Essentially my question is: how can I get a nice color distribution
while at the same time avoid the extreme scaling issues associated
with some data being zero (while all the other data is ~16)?

Thanks,
Jeremy

I am trying to plot a spectrum, with lower x axis = velocity, on the upper =
frequency

The relationship between them (doppler formula) is  
f = (1-v/c)*f_0 
where f is the resulting frequency, v the velocity, c the speed of light,
and f_0 the frequency at v=0, ie. the v_lsr.

I have tried to solve it by looking at  
http://matplotlib.sourceforge.net/examples/axes_grid/parasite_simple2.html
http://matplotlib.sourceforge.net/examples/axes_grid/parasite_simple2.html 
, where it is solved by 

pm_to_kms = 1./206265.*2300*3.085e18/3.15e7/1.e5
aux_trans = matplotlib.transforms.Affine2D().scale(pm_to_kms, 1.)
ax_pm = ax_kms.twin(aux_trans)
ax_pm.set_viewlim_mode("transform")

well, my problem is that it is not a simple scaling law, but a linear
function.

Anyone know how to solve this?

Magnus
-- 
View this message in context: http://old.nabble.com/Twiny-and-affine-transform-for-xlim-tp29032627p29032627.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Hi,

Thanks for the suggestions.  I also came the same conclusion about ordering
the arrays before hand.  This did the trick for the zorder, but I also have
to make the marker unique for each data point. I need to keep everything
into one artist since I'm using a pick event to display the data represented
by that point.  I'm not sure how I can use just 1 Artist, but get a variety
of distinct shapes (circles, squares, and triangles should be sufficient).

Thanks so much!
Aman

PS. Sorry about the duplicate emails Jeff.  I forgot to hit "Reply to All"
the first time.

On Tue, Jun 29, 2010 at 3:39 PM, Jeff Whitaker <js...@fa...> wrote:

>  On 6/29/10 1:19 PM, Thomas Lecocq wrote:
>
> Hi,
>
> What about ordering the arrays before plotting ? Are the first elements
> drawn back to front ?
>
> Thomas
>
> **********************
> Thomas Lecocq
> Geologist
> Ph.D.Student (Seismology)
> Royal Observatory of Belgium
> **********************
>
>
>
> ------------------------------
> Date: Mon, 28 Jun 2010 12:55:22 -0400
> From: ath...@we...
> To: mat...@li...
> Subject: [Matplotlib-users] zorder for individual points in a scatter plot
> on a Basemap
>
> Hi,
>
> I'm currently using a scatter plot on a Basemap and I'd like to set the
> zorder of the individual points based on their temperature.   The higher the
> temperature, the higher the zorder.  Also, i'm  using a colorbar to set the
> colors for the plot.  Here is a snippet of my code:
>
>         x = np.array(val)
>         fig.sca(ax1)
>         lon_0 =(urcrnrlon+llcrnrlon)/2
>         lat_0 =(urcrnrlat+llcrnrlat)/2
>         m =
> Basemap(llcrnrlon=llcrnrlon,llcrnrlat=llcrnrlat,urcrnrlon=urcrnrlon,
>
> urcrnrlat=urcrnrlat,resolution='i',projection='cyl',lon_0=lon_0,lat_0=lat_0)
>         m.drawcoastlines()
>         m.drawmapboundary()
>         m.drawparallels(np.arange(llcrnrlat-1,urcrnrlat+1,5.))
>         m.drawmeridians(np.arange(llcrnrlon-1,urcrnrlon+1,5.))
>         m.fillcontinents(color='white',lake_color='aqua')
>         m.drawcountries(linewidth=1)
>         lons,lats = m(lon,lat)
>
>         #I can do it this way, but this screws up the colorbar
>         #for i in range(len(x)):
>         #
> m.scatter(lons[i],lats[i],c=x[i],marker='o',picker=5,zorder=x[i])
>
>         m.scatter(lons,lats,c=x,marker='o',picker=5)
>         plt.title('Time Range: %s to %s'%(startDay.strftime("%b-%d
> %H:%M"),endDay.strftime("%b-%d %H:%M")))
>         plt.colorbar(shrink=0.5)
>
> Is there anyway to set the zorder of the points without using the loop in
> commented code? Any help would be greatly appreciated.
>
> Thanks,
>
>
> Aman:  You can save the mappable from the scatter you want the colorbar to
> represent, then pass that to colorbar.  i.e.
>
> im = m.scatter(lons,lats,c=x,marker='o',picker=5) # plot all the pts, save
> mappable
> # now do one at a time
>
> for i in range(len(x)):
>     m.scatter(lons[i],lats[i],c=x[i],marker='o',picker=5,zorder=x[i])
> plt.colorbar(im,shrink=0.5) # use mappable from 1st call to scatter for
> colorbar
>
> -Jeff
>
> --
> Jeffrey S. Whitaker         Phone  : (303)497-6313
> Meteorologist               FAX    : (303)497-6449
> NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
> 325 Broadway                Office : Skaggs Research Cntr 1D-113
> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>


-- 
Aman Thakral
B.Eng & Biosci, M.Eng Design

We have uploaded a tarball and Windows and OSX binaries of
matplotlib-1.0rc for testing

  http://drop.io/xortel1#

Please report bugs to the tracker:
http://sourceforge.net/tracker2/?group_id=80706

A few highlights:

* Closed over 100 bugs in past three months -- largely due to the
  heroic efforts of Eric Firing

* Faster magnification of large images, and the ability to zoom in
  to a single pixel

* axes_grid improvements

* Local installs of documentation work better

* tick_params -- makes it easier to control the properties and
locations of ticks

* Improved "widgets" -- mouse grabbing is supported

* Improved consistency between backends of the "show" function:
  blocking is more consistent and all backends can call it
  multiple times

* More accurate snapping of lines to pixel boundaries

* More consistent handling of color, particularly the alpha
  channel, throughout the API

* image based regression testing, buildbot tests triggered on svn commits

* JJs new gridspec is definitely worth a mention and a code
  snippet and/or screenshot (the trunkdocs link is currently
  broken
  http://matplotlib.sourceforge.net/trunk-docs/users/gridspec.html).
  In this context you may also mention Fernando's "subplots".

* enhanced annotation features.

* Ian's monumental contour fix: now contourf handles interior masked
  regions, and the boundaries of line and filled contours coincide


CHANGELOG since 0.99:

2010-06-20 Added Axes.tick_params and corresponding pyplot function
           to control tick and tick label appearance after an Axes
           has been created. - EF

2010-06-09 Allow Axes.grid to control minor gridlines; allow
           Axes.grid and Axis.grid to control major and minor
           gridlines in the same method call. - EF

2010-06-06 Change the way we do split/dividend adjustments in
           finance.py to handle dividends and fix the zero division bug reported
           in sf bug 2949906 and 2123566.  Note that volume is not adjusted
           because the Yahoo CSV does not distinguish between share
           split and dividend adjustments making it near impossible to
           get volume adjustement right (unless we want to guess based
           on the size of the adjustment or scrape the html tables,
           which we don't) - JDH

2010-06-06 Updated dateutil to 1.5 and pytz to 2010h.

2010-06-02 Add error_kw kwarg to Axes.bar(). - EF

2010-06-01 Fix pcolormesh() and QuadMesh to pass on kwargs as
           appropriate. - RM

2010-05-18 Merge mpl_toolkits.gridspec into the main tree. - JJL

2010-05-04 Improve backend_qt4 so it displays figures with the
           correct size - DSD

2010-04-20 Added generic support for connecting to a timer for events. This
           adds TimerBase, TimerGTK, TimerQT, TimerWx, and TimerTk to
           the backends and a new_timer() method to each backend's
           canvas to allow ease of creating a new timer. - RM

2010-04-20 Added margins() Axes method and pyplot function. - EF

2010-04-18 update the axes_grid documentation. -JJL

2010-04-18 Control MaxNLocator parameters after instantiation,
           and via Axes.locator_params method, with corresponding
           pyplot function. -EF

2010-04-18 Control ScalarFormatter offsets directly and via the
           Axes.ticklabel_format() method, and add that to pyplot. -EF

2010-04-16 Add a close_event to the backends. -RM

2010-04-06 modify axes_grid examples to use axes_grid1 and axisartist. -JJL

2010-04-06 rebase axes_grid using axes_grid1 and axisartist modules. -JJL

2010-04-06 axes_grid toolkit is splitted into two separate modules,
           axes_grid1 and axisartist. -JJL

2010-04-05 Speed up import: import pytz only if and when it is
           needed.  It is not needed if the rc timezone is UTC. - EF

2010-04-03 Added color kwarg to Axes.hist(), based on work by
           Jeff Klukas. - EF

2010-03-24 refactor colorbar code so that no cla() is necessary when
           mappable is changed. -JJL

2010-03-22 fix incorrect rubber band during the zoom mode when mouse
           leaves the axes. -JJL

2010-03-21 x/y key during the zoom mode only changes the x/y limits. -JJL

2010-03-20 Added pyplot.sca() function suggested by JJL. - EF

2010-03-20 Added conditional support for new Tooltip API in gtk backend. - EF

2010-03-20 Changed plt.fig_subplot() to plt.subplots() after discussion on
           list, and changed its API to return axes as a numpy object array
           (with control of dimensions via squeeze keyword). FP.

2010-03-13 Manually brought in commits from branch

  ------------------------------------------------------------------------
  r8191 | leejjoon | 2010-03-13 17:27:57 -0500 (Sat, 13 Mar 2010) | 1 line

  fix the bug that handles for scatter are incorrectly set when dpi!=72.
  Thanks to Ray Speth for the bug report.


2010-03-03 Manually brought in commits from branch via diff/patch
        (svnmerge is broken)

  ------------------------------------------------------------------------
  r8175 | leejjoon | 2010-03-03 10:03:30 -0800 (Wed, 03 Mar 2010) | 1 line

  fix arguments of allow_rasterization.draw_wrapper
  ------------------------------------------------------------------------
  r8174 | jdh2358 | 2010-03-03 09:15:58 -0800 (Wed, 03 Mar 2010) | 1 line

  added support for favicon in docs build
  ------------------------------------------------------------------------
  r8173 | jdh2358 | 2010-03-03 08:56:16 -0800 (Wed, 03 Mar 2010) | 1 line

  applied Mattias get_bounds patch
  ------------------------------------------------------------------------
  r8172 | jdh2358 | 2010-03-03 08:31:42 -0800 (Wed, 03 Mar 2010) | 1 line

  fix svnmerge download instructions
  ------------------------------------------------------------------------
  r8171 | jdh2358 | 2010-03-03 07:47:48 -0800 (Wed, 03 Mar 2010) | 1 line



2010-02-25 add annotation_demo3.py that demonstrates new functionality. -JJL

2010-02-25 refactor Annotation to support arbitrary Transform as xycoords
           or textcoords. Also, if a tuple of two coordinates is provided,
           they are interpreted as coordinates for each x and y position.
           -JJL

2010-02-24 Added pyplot.fig_subplot(), to create a figure and a group of
           subplots in a single call.  This offers an easier pattern than
           manually making figures and calling add_subplot() multiple times. FP

2010-02-17 Added Gokhan's and Mattias' customizable keybindings patch
           for the toolbar.  You can now set the keymap.* properties
           in the matplotlibrc file.  Newbindings were added for
           toggling log scaling on the x-axis. JDH

2010-02-16 Committed TJ's filled marker patch for
           left|right|bottom|top|full filled markers.  See
           examples/pylab_examples/filledmarker_demo.py. JDH

2010-02-11 Added 'bootstrap' option to boxplot. This allows bootstrap
           estimates of median confidence intervals. Based on an
           initial patch by Paul Hobson. - ADS

2010-02-06 Added setup.cfg "basedirlist" option to override setting
           in setupext.py "basedir" dictionary; added "gnu0"
           platform requested by Benjamin Drung. - EF

2010-02-06 Added 'xy' scaling option to EllipseCollection. - EF

2010-02-03 Made plot_directive use a custom PlotWarning category, so that
           warnings can be turned into fatal errors easily if desired. - FP

2010-01-29 Added draggable method to Legend to allow mouse drag
           placement.  Thanks Adam Fraser. JDH

2010-01-25 Fixed a bug reported by Olle Engdegard, when using
           histograms with stepfilled and log=True - MM

2010-01-16 Upgraded CXX to 6.1.1 - JDH

2009-01-16 Don't create minor ticks on top of existing major
           ticks. Patch by Neil Crighton. -ADS

2009-01-16 Ensure three minor ticks always drawn (SF# 2924245). Patch
           by Neil Crighton. -ADS

2010-01-16 Applied patch by Ian Thomas to fix two contouring
           problems: now contourf handles interior masked regions,
           and the boundaries of line and filled contours coincide. - EF

2009-01-11 The color of legend patch follows the rc parameters
           axes.facecolor and axes.edgecolor. -JJL

2009-01-11 adjustable of Axes can be "box-forced" which allow
           sharing axes. -JJL

2009-01-11 Add add_click and pop_click methods in
           BlockingContourLabeler. -JJL


2010-01-03 Added rcParams['axes.color_cycle'] - EF

2010-01-03 Added Pierre's qt4 formlayout editor and toolbar button - JDH

2009-12-31 Add support for using math text as marker symbols (Thanks to tcb)
           - MGD

2009-12-31 Commit a workaround for a regression in PyQt4-4.6.{0,1} - DSD

2009-12-22 Fix cmap data for gist_earth_r, etc. -JJL

2009-12-20 spines: put spines in data coordinates, add set_bounds()
           call. -ADS

2009-12-18 Don't limit notch size in boxplot to q1-q3 range, as this
           is effectively making the data look better than it is. - ADS

2009-12-18 mlab.prctile handles even-length data, such that the median
           is the mean of the two middle values. - ADS

2009-12-15 Add raw-image (unsampled) support for the ps backend. - JJL

2009-12-14 Add patch_artist kwarg to boxplot, but keep old default.
           Convert boxplot_demo2.py to use the new patch_artist. - ADS

2009-12-06 axes_grid: reimplemented AxisArtist with FloatingAxes support.
           Added new examples. - JJL

2009-12-01 Applied Laurent Dufrechou's patch to improve blitting with
           the qt4 backend - DSD

2009-11-13 The pdf backend now allows changing the contents of
           a pdf file's information dictionary via PdfPages.infodict. - JKS

2009-11-12 font_manager.py should no longer cause EINTR on Python 2.6
           (but will on the 2.5 version of subprocess). Also the
           fc-list command in that file was fixed so now it should
           actually find the list of fontconfig fonts. - JKS

2009-11-10 Single images, and all images in renderers with
           option_image_nocomposite (i.e. agg, macosx and the svg
           backend when rcParams['svg.image_noscale'] is True), are
           now drawn respecting the zorder relative to other
           artists. (Note that there may now be inconsistencies across
           backends when more than one image is drawn at varying
           zorders, but this change introduces correct behavior for
           the backends in which it's easy to do so.)

2009-10-21 Make AutoDateLocator more configurable by adding options
           to control the maximum and minimum number of ticks. Also
           add control of the intervals to be used for ticking. This
           does not change behavior but opens previously hard-coded
           behavior to runtime modification`. - RMM

2009-10-19 Add "path_effects" support for Text and Patch. See
           examples/pylab_examples/patheffect_demo.py -JJL

2009-10-19 Add "use_clabeltext" option to clabel. If True, clabels
           will be created with ClabelText class, which recalculates
           rotation angle of the label during the drawing time. -JJL

2009-10-16 Make AutoDateFormatter actually use any specified
           timezone setting.This was only working correctly
           when no timezone was specified. - RMM

2009-09-27 Beginnings of a capability to test the pdf backend. - JKS

2009-09-27 Add a savefig.extension rcparam to control the default
           filename extension used by savefig. - JKS

On 6/29/10 1:19 PM, Thomas Lecocq wrote:
> Hi,
>
> What about ordering the arrays before plotting ? Are the first 
> elements drawn back to front ?
>
> Thomas
>
> **********************
> Thomas Lecocq
> Geologist
> Ph.D.Student (Seismology)
> Royal Observatory of Belgium
> **********************
>
>
>
> ------------------------------------------------------------------------
> Date: Mon, 28 Jun 2010 12:55:22 -0400
> From: ath...@we...
> To: mat...@li...
> Subject: [Matplotlib-users] zorder for individual points in a scatter 
> plot on a Basemap
>
> Hi,
>
> I'm currently using a scatter plot on a Basemap and I'd like to set 
> the zorder of the individual points based on their temperature.   The 
> higher the temperature, the higher the zorder.  Also, i'm  using a 
> colorbar to set the colors for the plot.  Here is a snippet of my code:
>
>         x = np.array(val)
>         fig.sca(ax1)
>         lon_0 =(urcrnrlon+llcrnrlon)/2
>         lat_0 =(urcrnrlat+llcrnrlat)/2
>         m =     
> Basemap(llcrnrlon=llcrnrlon,llcrnrlat=llcrnrlat,urcrnrlon=urcrnrlon,
>                 
> urcrnrlat=urcrnrlat,resolution='i',projection='cyl',lon_0=lon_0,lat_0=lat_0)
>         m.drawcoastlines()
>         m.drawmapboundary()
>         m.drawparallels(np.arange(llcrnrlat-1,urcrnrlat+1,5.))
>         m.drawmeridians(np.arange(llcrnrlon-1,urcrnrlon+1,5.))
>         m.fillcontinents(color='white',lake_color='aqua')
>         m.drawcountries(linewidth=1)
>         lons,lats = m(lon,lat)
>
>         #I can do it this way, but this screws up the colorbar
>         #for i in range(len(x)):
>         #    
> m.scatter(lons[i],lats[i],c=x[i],marker='o',picker=5,zorder=x[i])
>
>         m.scatter(lons,lats,c=x,marker='o',picker=5)
>         plt.title('Time Range: %s to %s'%(startDay.strftime("%b-%d 
> %H:%M"),endDay.strftime("%b-%d %H:%M")))
>         plt.colorbar(shrink=0.5)
>
> Is there anyway to set the zorder of the points without using the loop 
> in commented code? Any help would be greatly appreciated.
>
> Thanks,
>

Aman:  You can save the mappable from the scatter you want the colorbar 
to represent, then pass that to colorbar.  i.e.

im = m.scatter(lons,lats,c=x,marker='o',picker=5) # plot all the pts, 
save mappable
# now do one at a time
for i in range(len(x)):
     m.scatter(lons[i],lats[i],c=x[i],marker='o',picker=5,zorder=x[i])
plt.colorbar(im,shrink=0.5) # use mappable from 1st call to scatter for 
colorbar

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi,

 

You can also use Numpy.gradient to compute the gradient , if e.g. your dx and dy aren't the same. 

 

Cheers, 

 

Thom

**********************
Thomas Lecocq 
Geologist
Ph.D.Student (Seismology)
Royal Observatory of Belgium
**********************


 
> Date: Tue, 29 Jun 2010 16:28:11 +0200
> From: mat...@li...
> To: mat...@li...
> Subject: Re: [Matplotlib-users] Displaying the gradient of an image
> 
> Hello,
> 
> I finally found the solution. It's as simple as:
> figure();
> imshow(img);
> pylab.quiver(U, V, units='x');
> 
> Mathieu
> 
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
 		 	   		  

Hi,

 

What about ordering the arrays before plotting ? Are the first elements drawn back to front ?

 

Thomas

**********************
Thomas Lecocq 
Geologist
Ph.D.Student (Seismology)
Royal Observatory of Belgium
**********************


 


Date: Mon, 28 Jun 2010 12:55:22 -0400
From: ath...@we...
To: mat...@li...
Subject: [Matplotlib-users] zorder for individual points in a scatter plot on a Basemap

Hi,

I'm currently using a scatter plot on a Basemap and I'd like to set the zorder of the individual points based on their temperature.   The higher the temperature, the higher the zorder.  Also, i'm  using a colorbar to set the colors for the plot.  Here is a snippet of my code:

        x = np.array(val)
        fig.sca(ax1)
        lon_0 =(urcrnrlon+llcrnrlon)/2
        lat_0 =(urcrnrlat+llcrnrlat)/2
        m =     Basemap(llcrnrlon=llcrnrlon,llcrnrlat=llcrnrlat,urcrnrlon=urcrnrlon,
                urcrnrlat=urcrnrlat,resolution='i',projection='cyl',lon_0=lon_0,lat_0=lat_0)
        m.drawcoastlines()
        m.drawmapboundary()
        m.drawparallels(np.arange(llcrnrlat-1,urcrnrlat+1,5.))
        m.drawmeridians(np.arange(llcrnrlon-1,urcrnrlon+1,5.))
        m.fillcontinents(color='white',lake_color='aqua')
        m.drawcountries(linewidth=1)
        lons,lats = m(lon,lat)
        
        #I can do it this way, but this screws up the colorbar
        #for i in range(len(x)):
        #    m.scatter(lons[i],lats[i],c=x[i],marker='o',picker=5,zorder=x[i])    
  
        m.scatter(lons,lats,c=x,marker='o',picker=5)    
        plt.title('Time Range: %s to %s'%(startDay.strftime("%b-%d %H:%M"),endDay.strftime("%b-%d %H:%M")))
        plt.colorbar(shrink=0.5)

Is there anyway to set the zorder of the points without using the loop in commented code? Any help would be greatly appreciated.

Thanks,

Aman
 		 	   		  

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I finally got it to work. I did the compilation of matplotlib with:
sudo make -f make.osx fetch deps mpl_build mpl_install
sudo python setup.py install

as described here:
http://blog.hyperjeff.net/?p=160

The first command correctly compiled matplotlib but installed it to
/usr/local. The second command incorrectly compiled matplotlib and installed
it in the Framework. Copying ft2font.so over from the /usr/local
installation fixed the problem "Abort trap" problem.


On Tue, Jun 29, 2010 at 9:56 AM, Ranjit Chacko <rjc...@gm...> wrote:

> I just recompiled freetype-2.4.12 and checked the version of
> /usr/local/lib/libfreetype.6.dylib with otool -l:
> Load command 3
>           cmd LC_ID_DYLIB
>       cmdsize 64
>          name /usr/local/lib/libfreetype.6.dylib (offset 24)
>    time stamp 1 Wed Dec 31 16:00:01 1969
>       current version 11.0.0
> compatibility version 11.0.0
>
> And I checked matplotlib's ft2font.so with otool -L:
>
> ft2font.so:
>     /usr/local/lib/libfreetype.6.dylib (compatibility version 11.0.0,
> current version 11.0.0)
>     /usr/local/lib/libz.1.dylib (compatibility version 1.0.0, current
> version 1.2.5)
>     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> version 7.9.0)
>     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 125.2.0)
>     /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> version 1.0.0)
>
> And now that they match I get "Abort trap" on loading matplotlib.pyplot and
> it looks as if ft2font.so has something to do with it:
>
>
> Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
> 0   libSystem.B.dylib                 0x00007fff84a893d6 __kill + 10
> 1   libSystem.B.dylib                 0x00007fff84b29972 abort + 83
> 2   libgcc_s.1.dylib                  0x0000000100487d51 uw_init_context_1
> + 385
> 3   libgcc_s.1.dylib                  0x00000001004884cc _Unwind_Resume +
> 76
> 4   ft2font.so                        0x00000001017b046d
> FT2Font::FT2Font(std::string) + 4269 (Extensions.hxx:629)
> 5   ft2font.so                        0x00000001017b0af8
> ft2font_module::new_ft2font(
>  Py::Tuple const&) + 408 (ft2font.cpp:1728)
> 6   ft2font.so                        0x00000001017b3d52
> Py::ExtensionModule<ft2font_module>::invoke_method_varargs(std::string
> const&, Py::Tuple const&) + 162 (Extensions.hxx:422)
> 7   ft2font.so                        0x00000001017c25a0
> method_varargs_call_handler + 512
>
> It looks like the sage developers encountered this problem and this is how
> they fixed it:
> http://trac.sagemath.org/sage_trac/ticket/7022
>
> All it does is take the plane vanilla matplotlib-0.99.1.spkg spkg and add a
> little script that simply rebuilds f2font.so again using *exactly* the same
> command lines used by distutils to build that extension. That's it. For some
> reason -- probably involving environment variables (?) -- this fixes the
> problem. I consider this a temporary 1-sage release solution until the
> matplotlib developers (or me) come up with a real fix.
>
> How do I rebuild f2font.so?
>
>
>
>>
>>

I just recompiled freetype-2.4.12 and checked the version of
/usr/local/lib/libfreetype.6.dylib with otool -l:
Load command 3
          cmd LC_ID_DYLIB
      cmdsize 64
         name /usr/local/lib/libfreetype.6.dylib (offset 24)
   time stamp 1 Wed Dec 31 16:00:01 1969
      current version 11.0.0
compatibility version 11.0.0

And I checked matplotlib's ft2font.so with otool -L:

ft2font.so:
    /usr/local/lib/libfreetype.6.dylib (compatibility version 11.0.0,
current version 11.0.0)
    /usr/local/lib/libz.1.dylib (compatibility version 1.0.0, current
version 1.2.5)
    /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
7.9.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
125.2.0)
    /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)

And now that they match I get "Abort trap" on loading matplotlib.pyplot and
it looks as if ft2font.so has something to do with it:


Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   libSystem.B.dylib                 0x00007fff84a893d6 __kill + 10
1   libSystem.B.dylib                 0x00007fff84b29972 abort + 83
2   libgcc_s.1.dylib                  0x0000000100487d51 uw_init_context_1 +
385
3   libgcc_s.1.dylib                  0x00000001004884cc _Unwind_Resume + 76
4   ft2font.so                        0x00000001017b046d
FT2Font::FT2Font(std::string) + 4269 (Extensions.hxx:629)
5   ft2font.so                        0x00000001017b0af8
ft2font_module::new_ft2font(
Py::Tuple const&) + 408 (ft2font.cpp:1728)
6   ft2font.so                        0x00000001017b3d52
Py::ExtensionModule<ft2font_module>::invoke_method_varargs(std::string
const&, Py::Tuple const&) + 162 (Extensions.hxx:422)
7   ft2font.so                        0x00000001017c25a0
method_varargs_call_handler + 512

It looks like the sage developers encountered this problem and this is how
they fixed it:
http://trac.sagemath.org/sage_trac/ticket/7022

All it does is take the plane vanilla matplotlib-0.99.1.spkg spkg and add a
little script that simply rebuilds f2font.so again using *exactly* the same
command lines used by distutils to build that extension. That's it. For some
reason -- probably involving environment variables (?) -- this fixes the
problem. I consider this a temporary 1-sage release solution until the
matplotlib developers (or me) come up with a real fix.

How do I rebuild f2font.so?



>
>

Hi all,

I am trying to change the labels of minor ticks, but leave the labels of the major ticks unchanged. To do this, I use the following function:

ax = plt.subplot(111)
ax.set_xticks([1,3,5])
ax.set_xticks([2,4], minor=True)
ax.set_xticklabels(["a", "b"], minor=True)

However, in result of the function both minor and major tick labels are changes. I checked the source code of XAxis.set_ticklabels and it contains following lines:

axis.py: lines 1335-1342

        if minor:
            self.set_minor_formatter(mticker.FixedFormatter(ticklabels))
            ticks = self.get_minor_ticks()
        else:
            self.set_major_formatter( mticker.FixedFormatter(ticklabels) )
            ticks = self.get_major_ticks()

        self.set_major_formatter( mticker.FixedFormatter(ticklabels) )

Note that the last lines sets the major tick formatter regardless of the "minor" argument. Is it intentional behaviour?

Yours,

Bartosz

Hello,

I finally found the solution. It's as simple as:
figure();
imshow(img);
pylab.quiver(U, V, units='x');

Mathieu

hi there,

I've got a bit stuck with running matplotlib in interactive mode.  maybe
what I want to do can't be done easily.

want I want is a simple python script which I can run with a file argument. 
this will then create some plots.  the script will wait for user input (via
sys.stdin.readline()), use the input to adjust a threshold and replot my
plots.  after the user is satisfied with the thresholds the script exit the
loop and will perform other processing.  Basically I'm trying to get a
simple interactive program with plots but without having use wxpython or
simliar

I have been trying to test the potting part of this.

I have successfully set interactive mode on and from the python interpreter
I can plot and I see my plots and updates to them without needing to use
pyplot.show().

when I run the same scripts by using 'python scriptname.py' I don't see the
plots unless I use pyplot.show().

my simple test script is as follows

############
#test interactive matplotlib plotting

import numpy as np
import sys
import matplotlib.pylab as pyp

a=np.array([0,4,5,5,3,4,5])
pyp.figure()
pyp.plot(a)
#pyp.show()
input=sys.stdin.readline()
pyp.xlabel('my xlabel %s' %input)
input=sys.stdin.readline()

any help much appreciated
-- 
View this message in context: http://old.nabble.com/matplotlib-in-interactive-mode-from-a-script-tp29023641p29023641.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

On Fri, Jun 11, 2010 at 8:49 PM, Eric Firing <ef...@ha...> wrote:

>> Do you have access to Sun SPARC hardware? If not, I can almost certainly arrange
>> access to a Sun T5240 (16 core) at the University of Washington for a serious
>> matplotlib developer.
>
> Dave,
>
> Thanks, but much as I would like to see this problem solved, I don't
> really want to get sucked into it.  I haven't messed with Suns for many
> years, and I am not eager to resume.
>
> Did you compile the previous version of matplotlib that you used on your
> machine, or did someone else there do it?
>
> Have you looked at the Cookbook entry?
> http://www.scipy.org/Cookbook/Matplotlib/CompilingMatPlotLibOnSolaris10

This issue is new and not related to the issue on the cookbook, I'm
pretty sure.  I have the same problem on my box at work, and it was
introduced when I upgraded to CXX6.  I have spent some time on it but
haven't found the fix yet.  I guess it's my bug :-(

I've added it to the tracker:

https://sourceforge.net/tracker/?func=detail&aid=3022815&group_id=80706&atid=560720

Hi Friedrich,

thanks a lot, that was exactly what I was looking for...


Alex

On Mon, Jun 28, 2010 at 23:00, Friedrich Romstedt <
fri...@gm...> wrote:

> 2010/6/28 Alexander Dietz <ale...@go...>:
> > I have a plot, to which I am drawing a colorbar. The standard colorbar
> > ranges from the values -1 (blue) over 0 (green) to e.g. 1(red). So far so
> > good.
> > But now I want to change the colorbar that it shows only the colors
> between
> > 0 and 1. What I mean is: the colorbar should start at value 0 (with
> green)
> > and go to 1(red), and leave the original plot unchanged.
>
> Ah, it wasn't that easy (for me).
>
> Friedrich
>

Hello,

I'm playing with some image processing algorithm (HOG descriptor) and 
I'm a bit lost. I am a newbie in image processing (especially in python).

I have computed the vertical and horizontal gradients of an image 
(convolution with [-1, 0, 1] on the 0 and 1 axis respectively). After 
that I computed the gradient' magnitude (sqrt(horizontal_gradient**2 + 
vertical_gradient**2)) and orientation (arctan2(vertical_gradient, 
horizontal_gradient)).

Now I would like to display the original image with the gradient vector. 
The quiver() function allows to plot vector fields and it's pretty easy 
to convert the gradient' magnitude and orientation into U and V (U 
=grad_mag*cos(grad_orientation), V = grad_mag*sin(grad_orientation)) but 
I cannot figure out how to display the image and the gradient with the 
right orientation.

Can anyone help?

Thanks in advance,
Mathieu

2010/6/29 Ranjit Chacko <rjc...@gm...>:
> I tried again by compiling version 2.4.11 of freetype instead of the latest
> and recompiling matplotlib with that and now I get the following less severe
> error:
>   Reason: Incompatible library version: ft2font.so requires version 11.0.0
> or later, but libfreetype.6.dylib provides version 10.0.0

Hmm, I'm using freetype 2.3.12 and yesterday it compiled fine with
this.  It guess it has some very simple reason, maybe you forgot to
remove the old compilation result or something like this?  :-) Good
luck,

Friedrich

I tried again by compiling version 2.4.11 of freetype instead of the latest
and recompiling matplotlib with that and now I get the following less severe
error:
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/pyplot.py",
line 6, in <module>
    from matplotlib.figure import Figure, figaspect
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/figure.py",
line 18, in <module>
    from axes import Axes, SubplotBase, subplot_class_factory
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axes.py",
line 12, in <module>
    import matplotlib.axis as maxis
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axis.py",
line 10, in <module>
    import matplotlib.font_manager as font_manager
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 52, in <module>
    from matplotlib import ft2font
ImportError:
dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/ft2font.so,
2): Library not loaded: /usr/local/lib/libfreetype.6.dylib
  Referenced from:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/ft2font.so
  Reason: Incompatible library version: ft2font.so requires version 11.0.0
or later, but libfreetype.6.dylib provides version 10.0.0



On Mon, Jun 28, 2010 at 5:43 PM, Ranjit Chacko <rjc...@gm...> wrote:

> I've been having some trouble with compiling matplotlib on Snow Leopard. I
> managed to get rid of all my old problems by recompiling everything with
> gcc-4.2.
>
> But now when I import matplotlib.pyplot I get an Abort trap message and
> python quits. Here is part of the error message I get:
>
> Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
> 0   libSystem.B.dylib                 0x00007fff84a893d6 __kill + 10
> 1   libSystem.B.dylib                 0x00007fff84b29972 abort + 83
> 2   libgcc_s.1.dylib                  0x0000000100487d51 uw_init_context_1
> + 385
> 3   libgcc_s.1.dylib                  0x00000001004884cc _Unwind_Resume +
> 76
> 4   ft2font.so                        0x00000001017b046d
> FT2Font::FT2Font(std::string) + 4269 (Extensions.hxx:629)
> 5   ft2font.so                        0x00000001017b0af8
> ft2font_module::new_ft2font(Py::Tuple const&) + 408 (ft2font.cpp:1728)
> 6   ft2font.so                        0x00000001017b3d52
> Py::ExtensionModule<ft2font_module>::invoke_method_varargs(std::string
> const&, Py::Tuple const&) + 162 (Extensions.hxx:422)
> 7   ft2font.so                        0x00000001017c25a0
> method_varargs_call_handler + 512
>
> It seems like freetype is the problem and from a little googling I see that
> the sage developers also had a problem with this. Does anyone know how to
> fix this?
>
> Thanks,
>
> -Ranjit
>
>

I've been having some trouble with compiling matplotlib on Snow Leopard. I
managed to get rid of all my old problems by recompiling everything with
gcc-4.2.

But now when I import matplotlib.pyplot I get an Abort trap message and
python quits. Here is part of the error message I get:

Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   libSystem.B.dylib                 0x00007fff84a893d6 __kill + 10
1   libSystem.B.dylib                 0x00007fff84b29972 abort + 83
2   libgcc_s.1.dylib                  0x0000000100487d51 uw_init_context_1 +
385
3   libgcc_s.1.dylib                  0x00000001004884cc _Unwind_Resume + 76
4   ft2font.so                        0x00000001017b046d
FT2Font::FT2Font(std::string) + 4269 (Extensions.hxx:629)
5   ft2font.so                        0x00000001017b0af8
ft2font_module::new_ft2font(Py::Tuple const&) + 408 (ft2font.cpp:1728)
6   ft2font.so                        0x00000001017b3d52
Py::ExtensionModule<ft2font_module>::invoke_method_varargs(std::string
const&, Py::Tuple const&) + 162 (Extensions.hxx:422)
7   ft2font.so                        0x00000001017c25a0
method_varargs_call_handler + 512

It seems like freetype is the problem and from a little googling I see that
the sage developers also had a problem with this. Does anyone know how to
fix this?

Thanks,

-Ranjit

2010/6/28 Alexander Dietz <ale...@go...>:
> I have a plot, to which I am drawing a colorbar. The standard colorbar
> ranges from the values -1 (blue) over 0 (green) to e.g. 1(red). So far so
> good.
> But now I want to change the colorbar that it shows only the colors between
> 0 and 1. What I mean is: the colorbar should start at value 0 (with green)
> and go to 1(red), and leave the original plot unchanged.

Ah, it wasn't that easy (for me).

Friedrich

It didn't work. But I may have misunderstood your instructions.
Here's the output from compiling matplotlib:
http://pastebin.org/363870

Here's what I did.
Set export CC=gcc-4.2
Set export MACOSX_DEPLOYMENT_TARGET=10.5

Downloaded and compiled libpng-1.4.3
Downloaded and compiled libfreetype-2.3.12
Downloaded matplotlib-0.99.3
Modified src/_png.cpp in matplotlib
Replaced setupext.py with your version.
sudo python setup.py build
sudo python setup.py install

Any obvious mistakes?

Thanks again for your help,

-Ranjit

On Mon, Jun 28, 2010 at 1:05 PM, Friedrich Romstedt <
fri...@gm...> wrote:

> 2010/6/28 Ranjit Chacko <rjc...@gm...>:
> > I just tried compiling with the following command:
> > sudo make -f make.osx fetch deps mpl_build mpl_install
>
> I don't know, I saw now so many people running into trouble with
> make.osx, would you, as a test case, please apply the following steps
> to your installation:
>
> First, I see that the freetype is linked in statically, but still it
> cannot be loaded on startup time (this _something_foobar symbol seems
> the first one it attemts to load).  I remember that make.osx is
> intended for binary distributable generation, and therefore it links
> statically.
>
> I want to propose a different solution here.
>
> Would you please modify first your matplotlib setupext.py in the
> following way.  We'll attemt a build without make.osx and fetch etc.,
> but a real distutil build with dynamic linking :-) !:
>
> On the line with 'darwin' : [], add:
>
>    'darwin' : ['/usr/local'],
>
> and maybe also '/usr/X11/lib' or '/usr/X11' and let the /lib suffix
> alone, but I think as you installed pkg-config, it could maybe work
> also out of the box.  For me, I were not aware of pkg-config for OS X,
> so I still don't have it :-).  If you are not sure, simply try to run
> pkg-config in the console, by tab expansion, if it finds it, it's
> installed.
>
> I also attach the modified files for your convenience, but you should
> use diff because I built that time 0.99.1.2, and something may have
> changed by that.
>
> Then, please compile (if you did not already do that), libpng 1.4 (not
> 1.2!) and libfreetype2 from the official sources.  Always use the
> following environment variables:
>
> export CC=gcc-4.2
> (To not use 4.0 occasionally)
> export MACOSX_DEPLOYMENT_TARGET=10.5
> (To avoid certain warnings which are quite annoying during build.  If
> you attemt to use py2app for deployment on 10.3 or 10.4 you should
> modify of course.)
>
> It is important that you compile *all* your software which is
> incorporated with the same variables.  Well, at least I by accident
> one time set _TARGET to another value after ./configure, and it
> refused to compile then.  So, feel free to experiment, but please
> document properly and, most important, tell us the results!  I'm still
> in the ascending branch of my OS X learning curve.
>
> Maybe now it's the right moment to compile Python (1.6.5, I think not
> 1.7) and then numpy again with this settings.  For Python, use
>
> ./configure --enable-framework
>
> Then compile libfreetype2.  Compile libpng 1.4 or whatever.
>
> Now it's time to compile matplotlib itself.  Just use the usual flags,
> and, for me, it worked like a charm.  But one modification has to be
> made: matplotlib isn't compatible with libpng 1.4 from the beginning,
> please add the following lines to src/_png.cpp:
>
> #define png_infopp_NULL (png_infopp)NULL
> #define int_p_NULL (int*)NULL
>
> Somewhere before the actual code, it doesn't matter where, but after
> the #include <png.cpp> of course.  I also attach the file, same
> applies, run diff before.  It's my obligation to provide a proper
> matplotlib patch for this issue, but for now please patch by hand.
>
> There are several reasons why to compile Python yourself: It will use
> the new Tcl/Tk, which is much more beautiful than the old one.  It
> will compile with the compatible flags.  Well that's it I think.  If
> you intend to use PIL btw, you have to compile Python yourself.
>
> Now you should be done.  If you run into some problems, please tell us.
>
> Friedrich
>